I've noticed a fair few anime villains/anti-heroes getting mentioned whenever a discussion like this comes up, and while I don't watch much anime, I do have to listen to endless lectures on various characters and their bizarrely contrived motivation. I've come to the conclusion that...perhaps...anime is really not the bastion of excellent characterisation and writing that I have been informed it is, and that maybe it really is just cartoons with excessive gore.
In terms of those characters, it always comes down to a sense of scale, doesn't it? Batman fights criminals out of some sense of revenge for his dead parents, while Anime Villain wants to destroy the world because someone was mean to him one time. Also there's the old "let's take creepy things, apply them to usually non-creepy things, and create TEN YEAR OLD MURDERER-RAPIST TWINS!"
I forget which anime that is. Begins with an H, I think.
What I'm trying to say, I think, is that anime characters totally shouldn't count in this thread because their motivations are often far too contrived and forced to be legitimately, in-fiction incomprehensible, and are just plain silly.
On a more relevant note, and eerily similar to the whole complaint about anime up there, look at the villains from Modern Warfare 2 and 3. This character wanted war, for whatever reason, so they staged a massacre and RUSSIA STEAMROLLED OVER EUROPE AND INVADED THE US! (From a really strange entry point)